Persistent URLs Research Articles

A Comprehensive Evaluation of Data Quality in Nutrient Databases.

Nutrient databases are a critical component of nutrition science and the basis of exciting new research in precision nutrition (PN). To identify the most critical components needed for improvement of nutrient databases, food composition data were analyzed for quality, with completeness being the most important measure, and for FAIRness, how well the data conformed with the data science criteria of findable, accessible, interoperable, and reusable (FAIR). Databases were judged complete if they provided data for all 15 nutrition fact panel (NFP) nutrient measures and all 40 National Academies of Sciences, Engineering, and Medicine (NASEM) essential nutrient measures for each food listed. Using the gold standard the USDA standard reference (SR) Legacy database as surrogate, it was found that SR Legacy data were not complete for either NFP or NASEM nutrient measures. In addition, phytonutrient measures in the 4 USDA Special Interest Databases were incomplete. To evaluate data FAIRness, a set of 175 food and nutrient data sources were collected from worldwide. Many opportunities were identified for improving data FAIRness, including creating persistent URLs, prioritizing usable data storage formats, providing Globally Unique Identifiers for all foods and nutrients, and implementing citation standards. This review demonstrates that despite important contributions from the USDA and others, food and nutrient databases in their current forms do not yet provide truly comprehensive food composition data. We propose that to enhance the quality and usage of food and nutrient composition data for research scientists and those fashioning various PN tools, the field of nutrition science must step out of its historical comfort zone and improve the foundational nutrient databases used in research by incorporating data science principles, the most central being data quality and data FAIRness.

Ending Law Review Link Rot: A Plea for Adopting DOI

Though the vast majority of law reviews are now published online, very few law review publishers use persistent URLs, like DOI, to provide stable online access. The purpose of this article is to encourage law reviews to implement DOI, and demystifies the process for doing so.

Persistent URLs and Citations Offered for Digital Objects by Digital Libraries

As libraries, archives, and museums make unique digital collections openly available via digital library platforms, they expose these resources to users who may wish to cite them. Often several URLs are available for a single digital object, depending on which route a user took to find it, but the chosen citation URL should be the one most likely to persist over time. Catalyzed by recent digital collections migration initiatives at Indiana University Libraries, this study investigates the prevalence of persistent URLs for digital objects at peer institutions and examines the ways their platforms instruct users to cite them. This study reviewed institutional websites from the Digital Library Federation’s (DLF) published list of 195 members and identified representative digital objects from unique digital collections navigable from each institution’s main web page in order to determine persistent URL formats and citation options.
 Findings indicate an equal split between offering and not offering discernible persistent URLs with four major methods used: Handle, DOI, ARK, and PURL. Significant variation in labeling persistent URLs and inclusion in item-specific citations uncovered areas where the user experience could be improved for more reliable citation of these unique resources.

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain a coherent RDF graph the chosen ontology must be consistently applied. However, addition of new diverse data causes the ontology to evolve, which could lead to accumulation of unintended erroneous composites. Thus, there is a need for a gate keeping system that compares the intended content described in the ontology with the actual content of the resource. The Empusa code generator facilitates creation of composite RDF resources from disparate sources. Empusa can convert a schema into an associated application programming interface (API), that can be used to perform data consistency checks and generates Markdown documentation to make persistent URLs resolvable. Using Empusa consistency is ensured within and between the ontology and the content of the resource. As an illustration of the potential of Empusa, we present the Genome Biology Ontology Language (GBOL). GBOL uses and extends current ontologies to provide a formal representation of genomic entities, along with their properties, relations and provenance.

RNPLS&T’s e-library: The history, development dynamics, technologies, and resources

The history of RNPLS&T E-library and Electronic Archive of heterogeneous information resource since 2006 is discussed. Development of RNPLS&T’s in-house digital resources is also examined. Special attention is given to the E-library development dynamics in 2011–2018. The most popular thematic collections for 2017 are analyzed. The Electronic Archive technological platform for digitized documents processing, hosting, storing and presenting is discussed in detail. The authors argue that with implementing the Electronic Archive the efficiency of digital books generation increased due to universal operator interface, which enables to prepare and host digital documents on several workstations. The technology of incoming documents processing for RNPLS&T’s E-library is based on the IRBIS64 LAS technologies and RNPLS&T’s E-catalog and enables to extract entries generated within a given time period. The technology specific feature is that in every extracted bibliographic record, digitized resource URL is changed to PURL (Persistent URL), which enables to relocate, if necessary, the digitized documents to another depository without changing its bibliographic description.The relevance of user demanded documents from the RNPLS&T’s E-library is analyzed.The authors acknowledge that RNPLS&T’s E-library resources in engineering make a significant part of the digital resources of the National Electronic Library.

BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud.

BioJupies is a web application that enables the automated creation, storage, and deployment of JupyterNotebooks containing RNA-seq data analyses. Through an intuitive interface, novice users can rapidly generate tailored reports to analyze and visualize their own raw sequencing files, gene expression tables, or fetch data from >9,000 published studies containing >300,000 preprocessed RNA-seq samples. Generated notebooks have the executable code of the entire pipeline, rich narrative text, interactive data visualizations, differential expression, and enrichment analyses. The notebooks are permanently stored in the cloud and made available online through a persistent URL. The notebooks are downloadable, customizable, and can run within a Docker container. By providing an intuitive user interface for notebook generation for RNA-seq data analysis, starting from the raw reads all the way to a complete interactive and reproducible report, BioJupies is a useful resource for experimental and computational biologists. BioJupies is freely available as a web-based application from http://biojupies.cloud.

Reproducible, component‐based modeling with TopoFlow, a spatial hydrologic modeling toolkit

Modern geoscientists have online access to an abundance of different data sets and models, but these resources differ from each other in myriad ways and this heterogeneity works against interoperability as well as reproducibility. The purpose of this paper is to illustrate the main issues and some best practices for addressing the challenge of reproducible science in the context of a relatively simple hydrologic modeling study for a small Arctic watershed near Fairbanks, Alaska. This study requires several different types of input data in addition to several, coupled model components. All data sets, model components and processing scripts (e.g., for preparation of data and figures, and for analysis of model output) are fully documented and made available online at persistent URLs. Similarly, all source codes for the models and scripts are open source, version controlled, and made available online via GitHub. Each model component has a Basic Model Interface to simplify coupling and its own HTML help page that includes a list of all equations and variables used. The set of all model components (TopoFlow) has also been made available as a Python package for easy installation. Three different graphical user interfaces for setting up TopoFlow runs are described, including one that allows model components to run and be coupled as web services.

A Computational Model Library for publishing model documentation and code

We present a repository for disseminating the computational models associated with publications in the social and life sciences. The number of research projects using computational models has been steadily increasing but the resulting publications often lack model code and documentation which hinders replication, verification of results and accumulation of knowledge. We have developed an open repository, the CoMSES Net Computational Model Library, to address this problem. Submissions to the library can be original models accompanying publications or replications of previous studies. Researchers can request that their models undergo a certification process that verifies that the model code successfully compiles and runs and that it follows documentation best practices. Models that pass the certification process are assigned persistent URLs and identifiers. We present the basic components of our repository, discuss our initial experiences with the library, and elaborate on future steps in the development of this cyberinfrastructure.

Electronic Theses and Dissertations Initiatives: A Survey of University Libraries in Nigeria

The study investigated the extent of adoption of electronic theses and dissertations in university libraries in Nigeria. Data collection for the study was via online questionnaire. The study revealed that digitization of theses and dissertations started between 1980 and 1995. It was found that only a few university libraries have embraced digitization of theses and dissertations in Nigeria. Benefits of electronic theses and dissertations were identified as improving university ranking and visibility, increasing access to the theses and dissertations, saving space in the library, enabling others link to the work with persistent URLs, preserving the work for future generations, and saving costs for students. Challenges such as unstable internet connectivity, lack of funding, irregular power supply, lack of information technology personnel, absence of electronic theses and dissertations submission policy, and copyright issues were identified. It is hoped that the study might provide insights useful for librarians planning to embark on the digitization of theses and dissertations project.

Free U.S. Government Databases for Non-Depository Libraries

Free federal government databases are an untapped resource of which many libraries do not take advantage. Many of the databases are cataloged and can be added to a library Online Public Access Catalog; other databases have persistent URLs that can be linked from LibGuides or other online subject finding aids. The desirability and potential drawbacks of adding these resources to the catalog are discussed. Before referring library users to the databases, evaluative criteria must be applied to ensure stability, authority, currency, and ease of search. A select list of federal agency databases that meet the criteria is offered.

OpenART: Open metadata for art research at the tate

AbstractEditor's SummaryThe short‐term OpenART project was geared to exposing linked open data for the research dataset, “The London Artworld 1660‐1735,” of the Tate Britain art gallery, enabling viewers to learn about activities in the art world of the times. Work for the project required decisions and choices about using open data, starting with considering use cases and identifying entities and relationships. The dataset was modeled and expressed in the Resource Description Framework, using an event – art sales – as the central component of the model. An OpenART ontology was developed to provide domain‐specific descriptors and integrated with existing ontologies to provide semantic interoperability. The resulting event‐based ontology supported reciprocal statements about entities revolving around an event, as well as references back to other types of information for greater detail. Data was transformed from spreadsheets to RDF documents, served to a data repository and provided with persistent URLs. The OpenART project demonstrated practical approaches to exposing linked open data while enabling sharing and creative reuse of the research data.

Sharing and archiving nucleic acid structure mapping data

Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu.

Knowing Where They Went: Six Years of Online Access Statistics via the Online Catalog for Federal Government Information

As federal government information is increasingly migrating to online formats, libraries are providing links to this content via URLs or persistent URLs (PURLs) in their online public access catalogs (OPACs). Clickthrough statistics that accumulated as users visited links to online content in the University of Denver’s library OPAC were gathered over a six-year period and were analyzed. Among the conclusions were that DU users prefer online content over print for both newer and older documents and that there is great benefit in adding URLs above and beyond the URLs supplied by GPO cataloging.

Using a Local Electronic Resource Management System to Manage E-journals: Can It Get Any Better Than This?

The Smithsonian Institution Libraries (SIL) use a locally developed and maintained database for managing electronic resources. Journal and database titles, vendors, interlibrary loan, usage, and SIL persistent URLs are collected and tracked for free and subscribed content in one central access tool. This session discussed the current workflows along with the pros and cons of such an arrangement, and some possible future directions for SIL.

Aggravating or Aggregating? Providing Effective Access to Contents of Aggregator Databases: A Reference/Collection Development Librarian's Perspective

ABSTRACT Based on his experience, the author summarizes what reference/collection development librarians and library users want and expect from aggregator databases, and what's needed from database vendors and from librarians to meet these expectations. Particularly important are content quality, reliability, modularity, and affordability, interface simplicity and flexibility, and reliable congruence between and integration of print and electronic editions. From vendors, librarians should demand more and better content guarantees, purchase options, communication of content details and changes, full-text searching, and persistent URLs for individual titles. Librarians should provide analyzed cataloging and holdings for all titles in aggregator databases, keep these records current, fully integrate them with records for print and other electronic editions, and incorporate them into web catalogs, in addition to providing other web access tools such as browsable title lists.